ayout 1 - EMBL Grenoble

EMBL-EBI
PANDA proteins and the Apweiler research
group
Previous and current research
The PANDA (Protein and Nucleotide Data) group was created in June 2007 by merging the former
Ensembl (Birney) and Sequence Database (Apweiler) groups.
The activities of the PANDA group are focussed on the production of protein sequence, protein
family and nucleotide sequence databases at EMBL-EBI. We maintain and host the EMBL Nucleotide
Sequence Database, the Ensembl genome browser, the UniProt protein resource, and a
range of other biomolecular databases. These efforts can be divided into three major groups: nucleotides,
proteins, and chemoinformatics and metabolism. In addition to PANDA activities, the
Apweiler group has a complementary research component.
The activities of the PANDA proteins teams are centred on the mission of providing public access
to all known protein sequences and functional information about these proteins. The UniProt resource
provides the centrepiece for these activities. Most of the UniProt sequence data is derived
from translation of nucleotide sequences provided by the European Nucleotide Archive and Ensembl. All UniProt data undergoes classification
provided by InterPro (see the report from Sarah Hunter, page 78). In addition, we add information extracted from the scientific literature
and curator-evaluated computational analysis whenever possible. The combined InterPro literature annotation forms the basis for
automatic annotation approaches to annotate all the sequence data without experimental functional data. Protein interaction and identification
data is or will be provided to UniProt by the IntAct protein–protein interaction database and by the Protein Identification (PRIDE) database.
Ongoing research activities in the group include the development of methods to improve searching of large biological datasets, approaches
to improve protein identification from mass spectrometry data, algorithms for genome-wide sequence comparison and the development of
tools for the automatic annotation of proteins.
Future projects and goals
Rolf Apweiler
PhD 199, University of
Heidelberg. Germany.
Team leader at EMBL-EBI
since 1997.
It is our intention to work on improved integration and synchronisation of all PANDA resources. Despite the abundance of data from largescale
experimentation on a genome-wide level, such as expression profiling, protein–protein interaction screens or protein localisation, the
systematic and integrated use of this type of information for high-throughput annotation of proteins remains largely unexplored. We therefore
intend to build on ongoing research activities at EMBL-EBI to develop and assess new protocols to integrate and analyse functional genomics
datasets for the purpose of high-throughput annotation of uncharacterised proteins. This will include the analysis of different data
types regarding their suitability for the approach, development of data structures that allow the efficient integration and mining of data of different
types and quality as well as benchmarking of the obtained results and the application of new methodologies to the annotation of UniProtKB/TrEMBL
records.
Selected references
Klie, S. et al. (2008). Analyzing large-scale proteomics projects with
latent semantic indexing. J. Proteome Res., 7, 182-191
Mueller, M. et al. (2008). Analysis of the experimental detection of
central nervous system-related genes in human brain and
cerebrospinal fluid datasets. Proteomics, 8, 1138-118
The UniProt Consortium (2008). The Universal Protein Resource
(UniProt). Nucleic Acids Res., 36, D190-195
Mueller, M. et al. (2007). Annotating the human proteome: Beyond
establishing a parts list. Biochimica et Biophysica Acta, 177, 175-
191
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